Bioethanol Boom or Bust

Ethanol structureBioethanol, or strictly speaking cellulose-derived ethanol is fast becoming the front-runner in efforts to reduce our reliance on oil. There are problems associated with its production, not least issues of water supply and the environmental impact. The high production cost remains one of the biggest obstacles.

Now, researchers at Baylor University have identified forty different compounds formed in the pre-treatment step when making cellulosic ethanol that could be responsible for inhibiting the fermentation process, their elimination might reduce overall production costs and make this form of biofuel more economically viable.

“We screened for forty compounds, like phenols and organic acids, and they were all present,” said Kevin Chambliss, “We chose these particular compounds because they are believed to be inhibitory, but other compounds could be involved too.”

While conventional ethanol and cellulosic ethanol are essentially the same product, the two are made from different feedstocks. Conventional ethanol is produced from grains such as corn and wheat. Cellulosic ethanol is made from the non-food portion of many agricultural wastes. One of the more common wastes used is corn stover, which are the stalks and residue left over after harvest. Researchers said there has been a recent emphasis on learning more about cellulosic ethanol because agricultural wastes are mostly an untapped resource.

“If you can identify a pre-treatment condition that maximizes sugar production, yet minimizes inhibitor production, that could increase efficiency better than just removing the compound,” adds team member Peter van Walsum. The team will be testing softwood feedstocks, such as Dougas fir trees next.

InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3

DBPedia for Chemists

Taxol Total Synthesis Color

Cambridge chemist Peter Murray-Rust recently alerted me to the DBpedia service. DBpedia.org is a community effort to extract structured information (semantics) from Wikipedia and to make this information available on the Web. DBpedia allows you to ask sophisticated questions of Wikipedia rather than carrying out simple searches. “DBPedia is a semantic distillate of Wikipedia and soon all the chemistry will be in semantic form,” asserts Murray-Rust, “It will then be possible to ask questions like: “find compounds which were discovered by a Russian chemist in the 19th Century”. That is a simplistic example, of course. He believes that such efforts form part of a new information philosophy of linked data and points out that Open chemical resources, such as Pubchem, DBPedia, CrystalEye, ChEBI, etc. will soon become part of that philosophy.

Chemspy Blog Archived

Having run the Chemspy RSS feed manually for rather too long, we have finally upgraded to a CMS that enables a much slicker interface and will hopefully benefit readers considerably by providing easier access to the site news and our new chemistry news section. As such, earlier ChemSpy posts have now been archived as a standalone static page and can be accessed through the Chemspy chemistry news archives page here.

UPDATE: All chemistry items that would have originally been earmarked for inclusion in Chemspy will now appear in Sciencebase.com

Agony agonists and cancer combatants

Chemweb logoIn chemistry news this week, The Alchemist learns about slow-release drug formulations that prevent drug abuse, the risks of war associated with using depleted uranium in munitions and armour plating, and the analytical benefits of red wine that could turn up on labels to guide consumers to the most healthful Chianti or Zindanfel.

Also, this week, a well to wheel analysis reveals that hybrid cars are not as green as you would think and that converting natural gas to hydrogen for use in fuel cells could be the best environmental option for transport. Finally, web-savvy chemists using the Firefox browser have a new tool available to them that offers inline entries from blogs while they read ACS, RSC, Wiley, and other journal tables of contents.

This week’s grant goes to Bassam Shakhashiri for pioneering work in engaging the public with science and for helping to rebuild education programs after decimation by Reagan funding cuts in the 1980s.

Killer Shellfish – Domoic Acid

Domoic acidDomoic acid, a toxin produced by algae that can infest shellfish, is to blame for the recent spate of deaths from seafood poisoning, according to reports. The California Department of Health Services has detected elevated levels of domoic acid in sardines and mussels from coastal counties.

Domoic acid is synthesized by the microscopic alga, or diatom, Pseudo-nitzschia. Shellfish, including molluscs and crabs, ingest the algae, and so accumulate the toxin, ready to pass it on to some unsuspecting seafood diner. In large enough concentration, domoic acid causes amnesic shellfish poisoning. Symptoms occur within 24 hours and include vomiting, nausea, diarrhea and abdominal cramps. After a couple of days of such unpleasantness, short-term memory loss, dizziness, and confusion, can occur in severe cases as well as motor function problems, heart palpitations, and potentially coma and death.

Unfortunately, the toxin is not destroyed by cooking.

A total synthesis of domoic acid was carried out in 1982 by Yasufumi Ohfune and Masako Tomita of the Suntory Institute for Bioorganic Research, Japan, who corrected the initial structure report. (JACS, 1982, 104, 3511-3513).

InChI=1/C15H21NO6/c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/f/h17,19,21H

Raman and the usual substrates

My latest round up of science news over on SpectroscopyNOW.com is now online. This week, I discuss how a lot of protein research looks only at molecules at rest, but could be enriched so much more by observing how these biological molecules change step by step as they interact with each other and their usual substrates. Researchers at the European Synchrotron Radiation Facility (ESRF) and the Structural Biology Institute (IBS) have exploited the power of Raman spectroscopy to help them lock in on protein intermediates states that can then be snapped using X-rays from the synchrotron. The team can then piece together a stop-motion movie, in the style of Ray Harryhausen or Wallace and Gromit without the sword-wielding skeletons or sardonic dog.

Also in this week’s issue, dental researchers in London have demonstrated that the antibacterial solutions containing sodium hypochlorite (household bleach) and the calcium-sponge EDTA commonly used to clean up after root canal work, can actually destroy the organic content of the tooth’s dentine. I spoke to team leader, Kishor Gulabivala of the Eastman Dental Institute at University College London who pointed out that his team’s results have only so far been presented at a conference. Nevertheless, the research represents the first quantitative study of the effects of the antibacterial solutions on teeth, and suggest a need to reconsider their use in dental surgery.

Initially, I was concerned that it was their use in artificial teeth whitening that was the major issue, but Gulabivala assures me it is not. Despite this, I found several websites (amateur and otherwise) that suggest hypochlorite can be used as a bleaching agent for the teeth. Personally, I’d rather stick with yellow, stained teeth (if I happened to have them) rather than risking a mouthful of bleach.

A surgical robot that uses its own MRI scanner to pinpoint targets with microscopic precision also caught my eye for news on the SpectroscopyNOW MRI channel this week.

Ten years of online chemical community

Joao Aires de Sousa emailed me a while back to tell me that the excellent ORGLIST email discussion group was coming up to its tenth anniversary. I remember it was essential reading for bored staff in the editorial offices where I worked, providing light relief and a loose connection with the real world of chemistry happening beyond our admin system and manuscripts.

Trouble is, I got waylaid with other matters on the Sciencebase blog and overlooked Joao’s original post until last week, when I discovered that the tenth anniversary had been and gone. The first post was made on March 15, 1997 to announce the formation of the list and said simply “ORGLIST is a new mailing list dedicated to Organic Chemistry” and giving details on how to subscribe. Joao in this inaugural missive also asked everyone who received it to forward the email to potentially interested parties. Such was the extent of viral marketing in those days at a time when Youtube, Web 2.0, wikis, and blogs simply didn’t exist in the current sense.

The first “real” post was in French and asked about where to find information on the Blue Bottle experiment and the Ammonia Fountain, perennial high school science lab fodder, I believe.

A celebratory ORGLIST symposium entitled “Computers at the frontiers of Organic Chemistry” will be held this July 17 in parallel with the 7th National Meeting of Organic Chemistry of the Portuguese Chemical Society.

“Thousands of chemists from all over the world have gathered on ORGLIST to discuss Organic Chemistry,” Joao says.

I asked Joao about the longevity of the list. “Its success resides in email,” he says, “Email has a unique combination of features that make it extremely convenient. It is probably the Internet tool most integrated into the information processing routines of chemists.” He points out that checking email is pretty much a daily routine for almost everyone in science. “I think that makes email a great channel for building virtual networks of scientists,” he adds, “probably more than ever before!” Reaches the daily lives of hundreds of subscribers. “This allows quick, useful answers to posts and makes users feel part of a community,” Joao says, “That and ten years of online history.”

Chemical blogs, wikis, and quanta

I recently interviewed quantum chemist Steve Bachrach of Trinity University and asked him his thoughts on the web 2.0 revolution and whether or not chemists might benefit realistically from blogs and wikis.

“Well, this is really an issue of culture. My personal hesitancy to adopt Web 2.0 technologies is that I don’t have the time to read random thoughts by random individuals. I barely have time to keep up with the old-school (i.e., traditional journals) literature in my field. The blogosphere just seemed to me to be filled with the rantings of people who have nothing better to do with their time. Peter Murray-Rust’s blog was the first to demonstrate to me that real chemistry content could be had, that interesting and novel ideas could be found and shared and discussed.”

You can read the complete interview in the latest issue of Reactive Reports together with my regular round up of chemical science news for the site.

 Proteins’ Web of Intrigue  The latent strength of Miss Muffet’s arachnoid friend may have been in sexual allegory, but the image of a spider’s web as somehow weak, a glistening, gossamer netting for trapping only flies could not be further from the truth.

 Stem to Sperm  Stem cells from human bone marrow can be converted into early-stage sperm, according to a research team based at the North-east England Stem Cell Institute (NESCI), Newcastle.

 Dino Remains  We have not quite entered Jurassic Park, but researchers have successfully extracted protein from a 68 million year old Tyrannosaurus rex bone.

Cervical fluids and boron nitride

Two more reports of general interest from my SpectroscopyNOW column. The first is on a new informatics approach to understanding cervical vaginal fluids and the second on a new study of boron nitride the technological wonder material of the future
Screening for premature problems
The application of multiple protein identification algorithms to an analysis of cervical vaginal fluid (CVF) can provide a detailed map of biological markers to help researchers understand the course of human pregnancy and the problems that can arise. Preliminary tests suggest it could be used to determine the likelihood of a premature birth.

Inelastic boron nitride
The results of inelastic X-ray scattering and other techniques have been combined with ab initio calculations to characterise and explain the behaviour of the superficially simple binary material boron nitride. Insights from the research could lead to new ways to exploit the electronic and mechanical properties of hexagonal boron nitride.

Organic Kiwi Fruit

Organic kiwi fruitCould the claims of the “organic” farming movement be true after all? According to an international team who have analysed the antioxidant, mineral, and nitrate composition of kiwifruit, yes. Their findings published in the Journal of the Science of Food and Agriculture would suggest that growing the fuzzy green fruit using so-called organic principles leads to a higher content of health-promoting factors than those grown using conventional methods.

I asked team leader Adel Kader of the University of California, Davis, about his reasoning. “Most differences in composition between conventionally grown and organically grown fruits depend on differences in inputs,” he told us. These inputs include differences in fertilizers added and so results vary considerably from one study to the next, “In our kiwifruit study, the grower added more fertilizers to the organic kiwifruit plants than to the conventional ones and that is the reason for the higher mineral contents of the organic fruits,” he adds, “The one exception is phenolic [antioxidant] content, which has been shown in our study and in several other studies on a range of crops to be higher in organic than in conventional fruits.”

Kader believes that the difference is most likely due to the fruit having to survive against pests in the absence of synthetic pesticides. “Conventional agriculture practices utilize levels of pesticides that can result in a disruption of phenolic metabolites in the plant,” he says, “which have a protective role in plant defense mechanisms.” His hunch is further corroborated by the organic kiwifruit having thicker skins as well as the higher antioxidant activity which is thought to be a natural by-product of stress. He has a simple piece of advice for those dithering over whether to tuck into the fuzzy fruit: “My advice is that people eat more fruits regardless of whether they are conventionally or organically produced,” he told Sciencebase. More on this story in SpectroscopyNOW this week.